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(-) Description

Title :  CRYSTAL STRUCTURE OF TIBC-CATALYZED HYPER-GLYCOSYLATED TIBA55-350 FRAGMENT
 
Authors :  Q. Yao, Q. Lu, F. Shao
Date :  04 Apr 14  (Deposition) - 17 Sep 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Helix, Adhesion, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Lu, Q. Yao, Y. Xu, L. Li, S. Li, Y. Liu, W. Gao, M. Niu, M. Sharon, G. Ben-Nissan, A. Zamyatina, X. Liu, S. Chen, F. Shao
An Iron-Containing Dodecameric Heptosyltransferase Family Modifies Bacterial Autotransporters In Pathogenesis
Cell Host Microbe V. 16 351 2014
PubMed-ID: 25211077  |  Reference-DOI: 10.1016/J.CHOM.2014.08.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADHESIN/INVASIN TIBA AUTOTRANSPORTER
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 55-350
    Gene: TIBA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 316401
    Strain: ETEC H10407
    Synonym: ADHESIN/INVASIN TIBA, GLYCOPROTEIN TIBA, ADHESIN/INVASIN TIBA TRANSLOCATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 78)

Asymmetric Unit (2, 78)
No.NameCountTypeFull Name
128970Ligand/IonD-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 39)
No.NameCountTypeFull Name
128935Ligand/IonD-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 39)
No.NameCountTypeFull Name
128935Ligand/IonD-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (70, 70)

Asymmetric Unit (70, 70)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:74 , 289 A:402BINDING SITE FOR RESIDUE 289 A 401
02AC2SOFTWAREHIS A:72 , SER A:93 , 289 A:401 , 289 A:405BINDING SITE FOR RESIDUE 289 A 402
03AC3SOFTWARESER A:86 , GLY A:87 , 289 B:409BINDING SITE FOR RESIDUE 289 A 403
04AC4SOFTWARESER A:94 , GLY A:95 , 289 A:406BINDING SITE FOR RESIDUE 289 A 404
05AC5SOFTWARETYR A:91 , SER A:112 , 289 A:402 , 289 A:407BINDING SITE FOR RESIDUE 289 A 405
06AC6SOFTWARESER A:113 , 289 A:404 , 289 A:408 , 289 B:431BINDING SITE FOR RESIDUE 289 A 406
07AC7SOFTWAREHIS A:110 , HIS A:129 , SER A:131 , 289 A:405BINDING SITE FOR RESIDUE 289 A 407
08AC8SOFTWARESER A:132 , 289 A:406 , 289 A:409 , 289 B:430 , 289 B:431BINDING SITE FOR RESIDUE 289 A 408
09AC9SOFTWARESER A:151 , SER A:170 , 289 A:408 , 289 B:430 , 289 B:431BINDING SITE FOR RESIDUE 289 A 409
10BC1SOFTWAREGLY A:152 , GLY A:153 , SER A:154 , ALA A:155 , SER A:173 , ALA A:174 , THR A:175 , 289 A:434BINDING SITE FOR RESIDUE 289 A 410
11BC2SOFTWARESER A:170 , SER A:189 , 289 A:412BINDING SITE FOR RESIDUE 289 A 411
12BC3SOFTWARESER A:188 , SER A:189 , ARG A:207 , 289 A:411 , 289 A:413BINDING SITE FOR RESIDUE 289 A 412
13BC4SOFTWARESER A:189 , ASP A:208 , 289 A:412BINDING SITE FOR RESIDUE 289 A 413
14BC5SOFTWARETYR A:205 , ARG A:207 , SER A:226 , TYR A:245BINDING SITE FOR RESIDUE 289 A 414
15BC6SOFTWARESER A:227 , TYR A:245 , SER A:264 , 289 A:419BINDING SITE FOR RESIDUE 289 A 415
16BC7SOFTWARESER A:211 , SER A:230 , ALA A:232 , THR A:250BINDING SITE FOR RESIDUE 289 A 416
17BC8SOFTWARESER A:248 , ALA A:249 , THR A:250 , SER A:267 , THR A:269 , 289 B:424BINDING SITE FOR RESIDUE 289 A 417
18BC9SOFTWARETYR A:245 , SER A:263 , TYR A:282 , HOH A:518BINDING SITE FOR RESIDUE 289 A 418
19CC1SOFTWARESER A:264 , ASP A:284 , 289 A:415BINDING SITE FOR RESIDUE 289 A 419
20CC2SOFTWAREILE A:105 , SER A:124 , ASN A:143 , 289 B:416BINDING SITE FOR RESIDUE 289 A 420
21CC3SOFTWAREASN A:143 , SER A:162 , 289 A:422BINDING SITE FOR RESIDUE 289 A 421
22CC4SOFTWARESER A:162 , SER A:181 , 289 A:421 , 289 A:423BINDING SITE FOR RESIDUE 289 A 422
23CC5SOFTWARESER A:200 , ASN A:219 , THR A:220 , 289 A:422BINDING SITE FOR RESIDUE 289 A 423
24CC6SOFTWAREASN A:219 , SER A:238BINDING SITE FOR RESIDUE 289 A 424
25CC7SOFTWAREASN A:256 , SER A:275 , 289 A:426BINDING SITE FOR RESIDUE 289 A 425
26CC8SOFTWARESER A:294 , 289 A:425 , 289 A:427 , 289 B:422BINDING SITE FOR RESIDUE 289 A 426
27CC9SOFTWARESER A:313 , 289 A:426 , 289 B:421 , 289 B:422BINDING SITE FOR RESIDUE 289 A 427
28DC1SOFTWARESER A:322 , ALA A:323BINDING SITE FOR RESIDUE 289 A 428
29DC2SOFTWAREMSE A:156 , SER A:176 , ASN B:59 , THR B:61BINDING SITE FOR RESIDUE 289 A 429
30DC3SOFTWAREASN A:81 , SER A:100 , 289 A:431 , HOH A:521BINDING SITE FOR RESIDUE 289 A 430
31DC4SOFTWARESER A:119 , ASN A:138 , 289 A:430BINDING SITE FOR RESIDUE 289 A 431
32DC5SOFTWARESER A:97 , THR A:99 , THR A:118 , 289 A:433BINDING SITE FOR RESIDUE 289 A 432
33DC6SOFTWARESER A:116 , THR A:118 , 289 A:432 , 289 A:434BINDING SITE FOR RESIDUE 289 A 433
34DC7SOFTWAREGLY A:133 , SER A:135 , ALA A:136 , THR A:137 , SER A:154 , MSE A:156 , 289 A:410 , 289 A:433BINDING SITE FOR RESIDUE 289 A 434
35DC8SOFTWAREASP A:284 , ASN A:286 , SER A:305BINDING SITE FOR RESIDUE 289 A 435
36DC9SOFTWAREHIS B:72 , SER B:74 , 289 B:402BINDING SITE FOR RESIDUE 289 B 401
37EC1SOFTWAREHIS B:72 , SER B:93 , 289 B:401 , 289 B:405BINDING SITE FOR RESIDUE 289 B 402
38EC2SOFTWAREARG B:64 , SER B:86 , TYR B:255BINDING SITE FOR RESIDUE 289 B 403
39EC3SOFTWAREALA B:75 , SER B:94 , 289 B:406BINDING SITE FOR RESIDUE 289 B 404
40EC4SOFTWARETYR B:91 , SER B:112 , 289 B:402 , 289 B:407BINDING SITE FOR RESIDUE 289 B 405
41EC5SOFTWARESER B:113 , 289 B:404 , 289 B:408BINDING SITE FOR RESIDUE 289 B 406
42EC6SOFTWAREHIS B:110 , HIS B:129 , SER B:131 , 289 B:405 , HOH B:548BINDING SITE FOR RESIDUE 289 B 407
43EC7SOFTWARESER B:132 , 289 B:406 , 289 B:409BINDING SITE FOR RESIDUE 289 B 408
44EC8SOFTWARE289 A:403 , SER B:151 , 289 B:408BINDING SITE FOR RESIDUE 289 B 409
45EC9SOFTWARESER B:154 , ALA B:155 , MSE B:156 , SER B:173 , ALA B:174 , THR B:175 , LYS B:194BINDING SITE FOR RESIDUE 289 B 410
46FC1SOFTWAREILE B:169 , SER B:170 , 289 B:412BINDING SITE FOR RESIDUE 289 B 411
47FC2SOFTWAREILE B:169 , SER B:188 , ARG B:207 , 289 B:411 , 289 B:413BINDING SITE FOR RESIDUE 289 B 412
48FC3SOFTWARESER B:189 , ASP B:208 , 289 B:412BINDING SITE FOR RESIDUE 289 B 413
49FC4SOFTWAREARG B:207 , SER B:226 , TYR B:245 , HOH B:546BINDING SITE FOR RESIDUE 289 B 414
50FC5SOFTWARESER B:227 , TYR B:245 , SER B:264 , 289 B:419BINDING SITE FOR RESIDUE 289 B 415
51FC6SOFTWARE289 A:420 , SER B:230 , 289 B:417BINDING SITE FOR RESIDUE 289 B 416
52FC7SOFTWAREARG A:184 , SER B:248 , ALA B:249 , THR B:269 , 289 B:416BINDING SITE FOR RESIDUE 289 B 417
53FC8SOFTWARETYR B:245 , SER B:263 , SER B:264 , TYR B:282 , HOH B:519 , HOH B:534BINDING SITE FOR RESIDUE 289 B 418
54FC9SOFTWARESER B:264 , ASP B:284 , 289 B:415BINDING SITE FOR RESIDUE 289 B 419
55GC1SOFTWARESER B:124 , TYR B:274 , SER B:275 , THR B:293 , SER B:294 , 289 B:425 , 289 B:426 , HOH B:531BINDING SITE FOR RESIDUE 289 B 420
56GC2SOFTWARE289 A:427 , ASN B:143 , SER B:162 , 289 B:422 , 289 B:426 , 289 B:427BINDING SITE FOR RESIDUE 289 B 421
57GC3SOFTWARE289 A:426 , 289 A:427 , SER B:162 , SER B:181 , 289 B:421 , 289 B:423BINDING SITE FOR RESIDUE 289 B 422
58GC4SOFTWARESER B:200 , ASN B:219 , THR B:220 , 289 B:422BINDING SITE FOR RESIDUE 289 B 423
59GC5SOFTWARETHR A:269 , ASN A:270 , GLU A:289 , 289 A:417 , ASN B:219 , SER B:238 , HOH B:515BINDING SITE FOR RESIDUE 289 B 424
60GC6SOFTWAREASN A:270 , THR A:272 , ILE A:310 , ASN B:256 , SER B:275 , 289 B:420 , 289 B:426BINDING SITE FOR RESIDUE 289 B 425
61GC7SOFTWAREASN B:143 , SER B:275 , SER B:294 , 289 B:420 , 289 B:421 , 289 B:425 , 289 B:427 , HOH B:531BINDING SITE FOR RESIDUE 289 B 426
62GC8SOFTWAREASN B:143 , GLY B:163 , ARG B:203 , SER B:313 , 289 B:421 , 289 B:426 , HOH B:511 , HOH B:531BINDING SITE FOR RESIDUE 289 B 427
63GC9SOFTWARESER B:322 , HOH B:541 , HOH B:549BINDING SITE FOR RESIDUE 289 B 428
64HC1SOFTWARESER B:176BINDING SITE FOR RESIDUE 289 B 429
65HC2SOFTWARE289 A:408 , 289 A:409 , ASN B:81 , SER B:100 , 289 B:431BINDING SITE FOR RESIDUE 289 B 430
66HC3SOFTWARE289 A:406 , 289 A:408 , 289 A:409 , SER B:119 , ASN B:138 , 289 B:430BINDING SITE FOR RESIDUE 289 B 431
67HC4SOFTWARESER B:97 , THR B:99 , SER B:116 , THR B:118 , 289 B:433BINDING SITE FOR RESIDUE 289 B 432
68HC5SOFTWAREGLY B:114 , SER B:116 , SER B:135 , THR B:137 , 289 B:432 , 289 B:434BINDING SITE FOR RESIDUE 289 B 433
69HC6SOFTWARESER B:135 , THR B:137 , SER B:154 , 289 B:433BINDING SITE FOR RESIDUE 289 B 434
70HC7SOFTWAREASN B:286 , SER B:305 , ALA B:306 , ALA B:323 , SER B:326BINDING SITE FOR RESIDUE 289 B 435

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q1Q)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..ee.......eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeeee...eee..ee....eeeee...eee..ee....eeee....eee..ee....eeeee...eee..ee....eeeee..eeeeeee....eeee....eeeeeee....eeee....eeeeeee....eeee....eeeeeee....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q1q A  54 KAAYDNQTIGRGETSKSmHLSAGDTAKNTTINSGGKQYVSSGGSATSTTINIGGVQHVSSGGSATSSTINSGGHQHVSSGGSATNTTVNNGGRQTVFSGGSAmGTIINSGGDQYVISGGSATSASVTSGARQFVSSGGIVKATSVNSGGRQYVRDGGSATDTVLNNTGRQFVSSGGSAAKTTINSGGGmYLYGGSATGTSIYNGGRQYVSSGGSATNTTVYSGGRQHVYIDGNVTETTITSGGmLQVEAGGSASKVIQNSGGAVITNTSAAVSG 327
                                    63       |73        83        93       103       113       123       133       143       153  |    163       173       183       193       203       213       223       233       243       253       263       273       283       293   |   303       313       323    
                                            71-MSE                                                                              156-MSE                                                                               242-MSE                                                297-MSE                          


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..ee.......eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeee....eee..ee....eeeee...eee..ee....eeeee...eee..ee....eeee....eee..ee....eeeee...eee..ee....eeeee..eeeeeee....eeee....eeeeeee....eeee....eeeeeee....eeee....eee..ee....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q1q B  54 KAAYDNQTIGRGETSKSmHLSAGDTAKNTTINSGGKQYVSSGGSATSTTINIGGVQHVSSGGSATSSTINSGGHQHVSSGGSATNTTVNNGGRQTVFSGGSAmGTIINSGGDQYVISGGSATSASVTSGARQFVSSGGIVKATSVNSGGRQYVRDGGSATDTVLNNTGRQFVSSGGSAAKTTINSGGGmYLYGGSATGTSIYNGGRQYVSSGGSATNTTVYSGGRQHVYIDGNVTETTITSGGmLQVEAGGSASKVIQNSGGAVITNTSAAVSG 327
                                    63       |73        83        93       103       113       123       133       143       153  |    163       173       183       193       203       213       223       233       243       253       263       273       283       293   |   303       313       323    
                                            71-MSE                                                                              156-MSE                                                                               242-MSE                                                297-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Q1Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q1Q)

(-) Gene Ontology  (10, 10)

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    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TIBA_ECOH1 | Q9XD84
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 4Q1Q)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Q1Q)